Methods for genotyping

A method for genotyping one or more polymorphisms in a nucleic acid sample, where each polymorphism has a first and a second allele, comprising:

• amplifying the nucleic acid sample via polymerase chain reaction;
• incubating the amplified nucleic acid sample with one or more allele-specific capture probes to allow formation of complexes between target sequences and allele-specific capture probes, wherein the allele-specific capture probes comprise
• a target-specific region that terminates at its 3′ end with a base that is complementary to a polymorphic base in the target sequence,
• a tag region immediately adjacent the target-specific region, wherein each different allele-specific probe has a different sequence tag region, and
• wherein the 5′ ends of the allele-specific capture probes are connected to an initial solid support;
• extending the allele-specific capture probes in the presence of labeled nucleotides using the target sequence as a template to obtain labeled allele-specific capture probes, wherein extension of the allele-specific capture probes is blocked if there is a mismatch between the polymorphic position and the 3′ end of the allele-specific capture probe;
• cleaving the labeled allele-specific capture probes from the initial solid support, and hybridizing the labeled allele-specific capture probes with a subsequent solid support;
• and
• determining the genotype of said polymorphisms by determining which alleles are present, wherein the presence of labeled allele-specific capture probes is indicative of the presence of a particular allele in the nucleic acid sample.

A method of genotyping one or more polymorphisms in a nucleic acid sample comprising:

• amplifying the nucleic acid sample via polymerase chain reaction;
• mixing the amplified nucleic acid sample with one or more pairs of capture probes to form a mixture, wherein each pair of capture probes includes
• a first allele-specific primer having a first allele-specific region that is complementary to a first allele of a selected polymorphism and includes the polymorphic position, with a first tag region immediately 5′ of the first allele-specific region, and
• a second allele-specific primer having a second allele-specific region that is complementary to a second allele of the selected polymorphism and includes the polymorphic position, with a second tag region immediately 5′ of the second allele-specific region,
• wherein the first and second allele-specific primers omit common primer sequences 5′ of their respective allele-specific regions, and
• wherein the 5′ end of each capture probe is connected to an initial solid support;
• subjecting the mixture to a primer extension reaction, wherein said first and second allele-specific primers are extended with a DNA polymerase to generate first and second allele-specific extension products in the presence of the first and second alleles, respectively;
• cleaving the first and second allele-specific extension products from the initial solid support and hybridizing said first and second allele-specific extension products with a subsequent solid support, wherein the subsequent solid support is selected from the group consisting of arrays, beads, microparticles, microtiter dishes and gels;
• and
• detecting the presence of said first and second allele-specific extension products, wherein the presence of a first allele-specific extension product is indicative of the presence of the first allele of a selected polymorphism and the presence of a second allele-specific extension product is indicative of the presence of the second allele,
• wherein the first allele-specific primer comprises a first tag region, which is included in the first allele-specific extension product and the second allele-specific primer comprises a second tag region, which is included in the second allele-specific extension product, and
• wherein said first and second allele-specific extension products are associated with the subsequent solid support through hybridization between the tag regions and corresponding tag probes on the subsequent solid support.